Reproduction of selected plant varieties by tissue culture has been a commercial success for many years. The technique has enabled mass production of genetically identical selected ornamental plants, agricultural plants, and forest species. The woody plants in this last group have perhaps posed the greatest challenges. Some success with conifers was achieved in the 1970s using organogenesis techniques wherein a bud, or other organ, was placed on a culture medium where it was ultimately replicated many times. The newly generated buds were placed on a different medium that induced root development. From there, the buds having roots were planted in soil.
While conifer organogenesis was a breakthrough, costs were high due to the large amount of handling needed. There was also some concern about possible genetic modification. It was a decade later before somatic embryogenesis achieved a sufficient success rate so as to become the predominant approach to conifer tissue culture. With somatic embryogenesis, an explant, usually a seed or seed embryo, is placed on an initiation medium where it multiplies into a multitude of genetically identical immature embryos. These can be held in culture for long periods and multiplied to bulk up a particularly desirable clone. Ultimately, the immature embryos are placed on a development medium where they are intended to grow into somatic analogs of mature seed embryos. As used in the present description, a “somatic” embryo is a plant embryo developed by the laboratory culturing of totipotent plant cells or by induced cleavage polyembryogeny, as opposed to a zygotic embryo, which is a plant embryo removed from a seed of the corresponding plant. These embryos are then individually selected and placed on a germination medium for further development. Alternatively, the embryos may be used in artificial seeds, known as manufactured seeds.
There is now a large body of general technical literature and a growing body of patent literature on embryogenesis of plants. Examples of procedures for conifer tissue culture are found in U.S. Pat. Nos. 5,036,007 and 5,236,841 to Gupta et al.; U.S. Pat. No. 5,183,757 to Roberts; U.S. Pat. No. 5,464,769 to Attree et al.; and U.S. Pat. No. 5,563,061 to Gupta. Further, some examples of manufactured seeds can be found in U.S. Pat. No. 5,701,699 to Carlson et al., the disclosure of which is hereby expressly incorporated by reference. Briefly, a typical manufactured seed is formed of a seed coat (or a capsule) fabricated from a variety of materials such as cellulosic materials, filled with a synthetic gametophyte (a germination medium), in which an embryo surrounded by a tube-like restraint is received. After the manufactured seed is planted in the soil, the embryo inside the seed coat develops roots and eventually sheds the restraint along with the seed coat during germination.
One of the more labor intensive and subjective steps in the embryogenesis procedure is the selective harvesting from the development medium of individual embryos suitable for germination (e.g., suitable for incorporation into manufactured seeds). The embryos may be present in a number of stages of maturity and development. Those that are most likely to successfully germinate into normal plants are preferentially selected using a number of visually evaluated screening criteria. A skilled technician evaluates the morphological features of each embryo embedded in the development medium, such as the embryo's size, shape (e.g., axial symmetry), cotyledon development, surface texture, color, and others, and selects those embryos that exhibit desirable morphological characteristics. This is a highly skilled yet tedious job that is time consuming and expensive. Further, it poses a major production bottleneck when the ultimate desired output will be in the millions of plants.
It has been proposed to use some form of instrumental image analysis for embryo selection to supplement or replace the visual evaluation and classification described above. For example, International Patent Application No. PCT/US99/12128 (WO 99/63057), explicitly incorporated by reference herein, discloses a method for classifying somatic embryos based on images of embryos or spectral information obtained from embryos. Generally, the method develops a classification model (or a “classifier”) based on the digitized images or NIR (near infrared) spectral data of embryos of known embryo quality (e.g., potential to germinate and grow into normal plants, as validated by actual planting of the embryos and a follow-up study of the same or by the morphological comparison to normal zygotic embryos). A “classifier” is a system that identifies an input by recognizing that the input is a member of one of a number of possible classes. The classifier is then applied to image or spectral data of an embryo of unknown quality to classify the embryo according to its presumed embryo quality.
Various classification models, or classifiers, are available, such as Fisher's linear and quadratic discriminant functions, classification trees, k-nearest-neighbors clustering, neural networks, and SIMCA. All of these models have been successfully used in many applications, but have been found to perform below expectations when classifying embryos because they either fail to be fast enough or the data from the embryos do not meet the requirements for these classifiers to work.
PCT/US99/12128 (WO 99/63057), incorporated above, discloses an embryo classifier using a Lorenz curve and a Bayes optimal classifier, termed “Lorenz-Bayes” classifier. Furthermore, co-assigned U.S. Patent Application Publication No. 2005/0069176 describes a generalized form of Lorenz-Bayes classifier for classifying plant embryos. In addition, co-assigned U.S. Patent Application Publication No. 2006/0068372 describes a method of classifying plant embryos using penalized logic regression.
While these methods have been successful in rapidly and accurately classifying embryos according to their embryo quality, there is a continuing need to further increase the classification speed and accuracy in order to achieve mass classification required for mass production of manufactured seeds.